+Open data
-Basic information
Entry | Database: PDB / ID: 4ag1 | ||||||
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Title | Human Chymase - Fynomer Complex | ||||||
Components |
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Keywords | HYDROLASE/DE NOVO PROTEIN / HYDROLASE-DE NOVO PROTEIN COMPLEX / INHIBITOR / SERINE PROTEASE | ||||||
Function / homology | Function and homology information chymase / basement membrane disassembly / cytokine precursor processing / midbrain development / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / serine-type peptidase activity / secretory granule ...chymase / basement membrane disassembly / cytokine precursor processing / midbrain development / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / serine-type peptidase activity / secretory granule / cellular response to glucose stimulus / peptide binding / protein catabolic process / Signaling by SCF-KIT / cytoplasmic ribonucleoprotein granule / positive regulation of angiogenesis / regulation of inflammatory response / collagen-containing extracellular matrix / endopeptidase activity / intracellular membrane-bounded organelle / serine-type endopeptidase activity / extracellular space / extracellular region / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Schlatter, D. / Brack, S. / Banner, D.W. / Batey, S. / Benz, J. / Bertschinger, J. / Huber, W. / Joseph, C. / Rufer, A. / Van Der Kloosters, A. ...Schlatter, D. / Brack, S. / Banner, D.W. / Batey, S. / Benz, J. / Bertschinger, J. / Huber, W. / Joseph, C. / Rufer, A. / Van Der Kloosters, A. / Weber, M. / Grabulovski, D. / Hennig, M. | ||||||
Citation | Journal: Mabs / Year: 2012 Title: Generation, Characterization and Structural Data of Chymase Binding Proteins Based on the Human Fyn Kinase SH3 Domain. Authors: Schlatter, D. / Brack, S. / Banner, D.W. / Batey, S. / Benz, J. / Bertschinger, J. / Huber, W. / Joseph, C. / Rufer, A. / Van Der Klooster, A. / Weber, M. / Grabulovski, D. / Hennig, M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ag1.cif.gz | 211.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ag1.ent.gz | 170.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ag1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ag1_validation.pdf.gz | 443.6 KB | Display | wwPDB validaton report |
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Full document | 4ag1_full_validation.pdf.gz | 444.8 KB | Display | |
Data in XML | 4ag1_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 4ag1_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/4ag1 ftp://data.pdbj.org/pub/pdb/validation_reports/ag/4ag1 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25066.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P23946, chymase |
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#2: Protein | Mass: 9669.622 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli) |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Sequence details | ARTIFICIAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | pH: 5.5 / Details: 0.1 M BIS-TRIS PH 5.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 63158 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.54 % / Biso Wilson estimate: 22.42 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.51 |
Reflection shell | Resolution: 1.4→1.49 Å / Redundancy: 6.62 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.58 / % possible all: 99.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IN HOUSE STRUCTURE Resolution: 1.4→42.02 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.135 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED ANISOTRIPICALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.299 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→42.02 Å
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